[gmx-users] rerun under non-bonded E. terms

Albert Solernou a.solernou at leeds.ac.uk
Tue May 12 14:11:52 CEST 2015

I may have not expressed well my final goal. I need a trajectory, a .trr 
file, that has the forces. I am interested in the non-bonded forces of a 
sub-set of the residues, so I need to re-compute these, and cannot use 
the values that come from the full trajectory where all the residues are 

Thanks for your time,

On 05/12/2015 12:59 PM, Justin Lemkul wrote:
> On 5/12/15 7:57 AM, Albert Solernou wrote:
>> Thanks Justin,
>> still I would not know how to go from a .edr file into a trajectory 
>> that has the
>> forces of the atoms I am interested in.
> You don't.  The .edr file is the energy output of a simulation. If you 
> have your subtrajectory of interest, you'll get a new .edr file with 
> the quantities you want, if I understand your description.
> -Justin
>> Best,
>> Albert
>> On 05/12/2015 12:48 PM, Justin Lemkul wrote:
>>> On 5/12/15 7:46 AM, Albert Solernou wrote:
>>>> Well, back to the beginning, then.
>>>> Is there a way to do a re-run using only non-bonded energy terms? 
>>>> I'll explain a
>>>> bit further. I have a trajectory, and want to get a (sub)trajectory 
>>>> that has
>>>> only a sub-set of atoms and that accounts only for the non-bonded 
>>>> interactions
>>>> within this sub-set of atoms. So far, I have the extracted temporary
>>>> sub-trajectory that contains the solvent atoms as well as the 
>>>> residues I am
>>>> interested in. Is there an easy way to do that? Or should I modify 
>>>> the source
>>>> code, instead?
>>> The nonbonded terms don't depend on the bonded terms; they are, by 
>>> default,
>>> saved in the .edr file.  If you want some group-wise decomposition 
>>> (e.g.
>>> interaction energy) then that's what energygrps are for. There is no 
>>> need to
>>> modify code or hack the topology at all if this is what you're after.
>>> -Justin

   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds
   Tel: +44 (0)1133 431451

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